One of the issue that has arisen with the features on the site increasing is difficulty finding items later. A second issue is making things clearer for the non-technical person to understand if there is or is not an issue. If you are on the far left or far right of any of these chart — there is likely an issue.
I have just pushed an uber-page up which will display over 280 potential measures on microbiome samples — all measures are shown on charts with the values of other people who have shared their samples. If you are logged on, your values will be shown on the charts. All of these charts are on the same page, http://microbiomeprescription.azurewebsites.net/library/Distribution , but they contain different types of data.
I also switched to log(values) for the charts because of some extreme values. The key issue is not the number, but where you are compared to other samples. Using a log does not alter that.
Just select the condition that you are interested in.
This is a count of the bacteria that produces various end products. The information is incomplete (list is here).
This is an artifact set of charts from those that transcribed they data from uBiome. Their “1.0” for reference samples is totally suspect. These charts should indicate if you have an abnormal amount (far left or right).
I have included two ratios (and may add more upon request).
Taxa Counts in Reports
This was done earlier as ‘Quality of Sample’. It also gives an indication on the number of bacteria test for by various companies
There are a lot of charts but they are consolidated on one page with the ability to just scroll down and look at your sample values for each.
A reader reported a bug with the manual selection of which taxa to modify page that I did a while back. As a result, I smoothed the flow; I also realized that I need to allow a wider search for modifiers since the bacteria selected may have few known modifiers from studies– especially when a species or strain is selected. Site: http://microbiomeprescription.azurewebsites.net/
Quick Recap on how to Manual Select bacteria taxa
This is done via the “My Biome View” button from the Samples Page
On this page, you can select which taxa you wish to have included in the suggestions. You make the choices entirely.
Click the button and you will return to the Sample Page and a new button will appear:
This takes you to the usual custom suggestion page (except most of the bacteria filters are hidden — after all, you have hand picked them!)
Parent and children Modifiers are being added
Bacteria is reported in a hierarchy, the next level up is the parent, the next level down are the childern
Above you see that the Parent of Oscillibacter is Oscillospiraceae. Things reported to modify the parent will likely modify its children. The key work is likely. A modifier may reduce Marseillibacter but not Oscillibacter; we lack the studies.
Similarly, the three children of Oscillibacter may have items that modify them. One would expect that if something reduces one of the children then Oscillibacter would be reduced too! Again the key word is likely.
IF we have 10 or more modifier documented to change this bacteria, we do not include the parent or the children. If we have less than 10 then we include this additional information (giving it a reduced weight reflecting the greater uncertainty).
Do not ask me what is the right way to get suggestions. We do not know. What I can provide are tools that will generate suggestions is a logical manner. This latest addition extends the prior choices by:
Allowing you to hand pick the taxa from your sample, one by one
Allows you to extend the list of modifiers by asking to include items that modify its children (i.e. Lactobacillus Fermentum CQPC04 modifiers would be added to Lactobacillus Fermentum , OR/and its parent (i.e. Lactobacillus) if we have sparse information on how to modify it.
I expect only a few people will make use of this; but it is there if you want absolute control.
I have a regular task of manual reviewing potential studies selected by Textural Analysis (Artificial Intelligence/Data Science) published on PubMed. The count of articles reviewed by the AI and myself (for those that the AI selected) is up to 456,847 with many more to go. One of these articles listed the bacteria identified by this study (from human samples) that consumes/process gluten.
It is logical to hypothesis that gluten intolerance/issues is connected to the absence/low numbers of these bacterias.
A reader asks me to do a recap of what the known shifts are, and thus what you wish to try to correct (and not inadvertently increase by the wrong supplements, probiotics or diet choices).
In terms of published studies, I have assembled a dynamic list on my website (not verified and subject to data entry errors) shown below for genus level and above. When an item is repeated on multiple lines, this means that we have multiple studies report it. H-High, L- Low, B- High or Low (outside of normal)
At the Strain Level, we also have a long list,
Using the citizen science aspect of my site, we do not have a information based on physician verification of precise clinical definition but solely on self-reporting of symptoms. If click on one of the above, say Bifidobacterium, we see two things listed:
Citizen Science discoveries dealing with symptoms.
Published studies listing conditions that may have the same shift (thus, potential conditions that ME/CFS may evolve to).
For 1 (EBV),2 (MCS), 4(Female), 5, 6 (Post exertional malaise) are in the list of items that are used for a ME/CFS diagnosis
Going over to Faecalibacterium (3 citations) – another LOW one, we see a more massive symptom list, many many are in the classic ME/CFS diagnosis list.
Doing another one, Streptococcus – a HIGH one for a change (3 citations – 2 high and 1 low), we see
One list of bacteria comes from studies on patients that conform to strict definitions of ME/CFS. The other list of bacteria comes out of the symptoms people self-report and their 16s microbiome results. We have a very strong agreement with the results coming from two independent approaches.
What does this mean?
It means that altering the microbiome will improve symptoms (as indicated in the study cited at the start; and in personal agreement with my own experience and many of my readers).
The next step is to determine which of these long lists of bacteria is involved with your ME/CFS/IBS etc. The old conventional tests only does a few of the bacteria — and do not cover all of those reported in studies. By old conventional tests, I mean:
Once you know the bacteria involved, you need to know how to change them. If your physician, nutritionist or other health professional are well skilled and read on the microbiome, they should be able to guide you.
The Candida species play a role in a healthy body. It is when there is too many that problems start. A friend asked me to put together what we know based on published studies only, no urban-medical-beliefs.
There is an increased total fungal load particularly of Candida and Malassezia species in the faeces and mucosa of Crohn’s disease patients, and a lower fungal diversity in the faeces of ulcerative colitis patients. 
So to translate into familiar terms, in decreasing effectiveness:
These are cited, with further studies on this page (in french) and includes the above with links to multiple additional studies for each.
” It can be concluded that monolaurin has a potential antifungal activity against C. albicans and can modulate the pro-inflammatory response of the host. ” 
” The difference between the groups [chlorhexidine, lactobacillus probiotics, coconut oil] was not statistically significant (Chi-square value 7.42, P value 0.06). ” 
” Eucommia ulmoides, Polygonum cuspidatum, Poria cocos and Uncaria rhyncophylla showed activity against both bacterial and fungal strains, indicating their broad spectrum of activity. ” 
” Data show that mustard [i.e. Turmeric] and coconut oil seem to be effective as in these the spore germination was poor. ” 1992
Pau D’Arco ( Tabebuia ) – Studies found no significant effect 
“Tabebuia avellanedae (methanol extract), with MIC varying from 0.06 to 0.001 mg/mL; ”  – this is a fraction of the effectiveness of items above.
Enterococcus Faecalis appears effective  (available as probiotic)
Lactobacillus GG, Lactobacillus rhamnosus LC705 and Propionibacterium freudenreichii ssp. shermanii JS was shown to be an effective means of controlling oral Candida and hypo‐salivation in the elderly (Hatakka et al. 2007). 
Bacillus subtilis exhibited clear zones of inhibition for Candida albicans and Candida parapsilosis but not for Candida krusei. 
Sookkhee et al., in 2001, studied the effects on Candida albicans growth of different lactic-acid bacteria isolated from the oral cavity of volunteers and found that two strains, Lactobacillus paracasei and Lactobacillus rhamnosus, had the strongest effect on the yeast . Lactobacillus reuteriis a promising bacterium (especially DSM 17938 and ATCC PTA 5289) for its anti-Candida properties, confirmed by several studies. In one of these, Lactobacillus reuteri was demonstrated to be able to reduce Candida load in vivo through co-aggregation, modification of oral pH with production of lactic acid and other organic acids that inhibit the virulence of Candida cells, and production of H2O2 . In a recent in vitro study by Coman et al. (2014), the strains Lactobacillus rhamnosus IMC 501 and lactobacillus paracasei IMC 502, alone or in combination, showed an inhibitory effect on Candida spp. growth . Lactobacillus delbrueckii ssp. bulgaricus B1 and Lactobacillus delbrueckii ssp. bulgaricus TAB2 were found to fight Candida, releasing high amounts of lactic acid .Recently, it was found that Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 modulate Candida glabrata virulence, through the complete inhibition of fungal biofilms .In addition, Lactobacillus acidophilus ATCC 4356 was found to inhibit the biofilm formation of fungus through in vitro experiments . Biofilm formation is probably reduced through the production of substances called “bacteriocins” by probiotics. Wannun et al. reported the isolation of a bacteriocin, called “fermencin SD11”, from Lactobacillus fermentumSD11, a human oral Lactobacillus, which has a strong inhibitory effect on oral Candida cells .
Effect of Probiotics on Oral Candidiasis: A Systematic Review and Meta-Analysis 2019
All Lactobacillus Reuteri are histamine producers.
Many Bacillus subtilis are histamine producers 
Lactobacillus rhamnosus appears not to be a histamine producer and reduces histamines